Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1450 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg1205950486 sf1205949467 12 5950486 2.55E-08 3.79E-06
vg0103143509 sf0103142509 1 3143509 3.54E-08 5.84E-06
vg0907162669 sf0907161669 9 7162669 4.76E-08 NA
vg1217008330 sf1217002284 12 17008330 6.66E-08 NA
vg0103418043 sf0103417043 1 3418043 1.61E-07 NA
vg0819113876 sf0819111163 8 19113876 2.68E-07 NA
vg0401020004 sf0401015556 4 1020004 1.43E-06 NA
vg0818605378 sf0818602665 8 18605378 NA 3.18E-06
vg1013275525 sf1013204295 10 13275525 NA 3.24E-06
vg0406862676 sf0406858121 4 6862676 NA 5.85E-06